Novel polymerase compositions and uses thereof

ABSTRACT

The subject invention provides novel compositions containing a mixture of (a) an enzyme that possesses substantial 3′-5′ exonuclease activity (b) a DNA polymerase with less 3′-5′ exonuclease activity than the enzyme with substantial 3′-5′ exonuclease activity. Preferably, the DNA polymerase for inclusion in the compositions are DNA polymerases that substantially lack 3′-5′ exonuclease activity. A preferred embodiment of the invention is a composition comprising the Taq DNA polymerase (isolated from  Thermus aquaticus ) and the Pfu DNA polymerase (isolated from  Pyrococcus furiosus ). Another aspect of the invention is to provide methods for synthesizing polynucleotides, typically DNA, using compositions comprising an enzyme that possesses substantial 3′-5′ exonuclease activity and a DNA polymerase with less 3′-5′ exonuclease activity than the enzymes possessing substantial 3′-5′ exonuclease activity, preferably a DNA polymerase that substantially lacks 3′-5′ exonuclease activity. Another aspect of the invention involves the use the subject method of polynucleotide synthesis to carry out the synthesis step in a polymerase chain reaction experiment. Yet another aspect of the invention is to provide kits for the synthesis of polynucleotides, wherein the kits comprise an enzyme that possesses substantial 3′-5′ exonuclease activity and a DNA polymerase with less 3′-5′ exonuclease activity than the enzyme possessing substantial 3′-5′ exonuclease activity.

RELATED APPLICATIONS

This application is a continuation-in-part of co-pending U.S. patentapplication Ser. No. 08/164,290 which was filed Dec. 8, 1993.

FIELD OF THE INVENTION

The present invention is related to the field of molecular biology, andmore particularly, to polynucleotide synthesis.

BACKGROUND OF THE INVENTION

DNA polymerases catalyze the synthesis of DNA and can be found in allcells as well as being encoded in numerous viruses. Although all DNApolymerases possess 5′-3′ DNA polymerase activity, DNA polymerasesdiffer from one another in numerous other properties. For example, someenzymatic activities that are possessed by some DNA polymerases, butabsent in other DNA polymerases include: double stranded DNA 5′-3′exonuclease activity, single-stranded DNA 3′-5′ exonuclease activity,double-stranded 3′-5′ DNA exonuclease activity, RNase H activity,reverse transcriptase activity, and the like. Additionally, differentDNA polymerases may have different optimal pH and temperature ranges foractivity. Furthermore, DNA polymerases may differ in the rate in whichthey catalyze DNA synthesis.

Purified DNA polymerases have numerous uses in vitro. A detaileddescription of DNA polymerases, including methods for their isolation,can be found among other places, in DNA Replication 2nd edition, byKornberg and Baker, W.H. Freeman & Company, New York, N.Y. 1991. Invitro uses of DNA polymerases include, for example, the labeling andsynthesis of hybridization probes, DNA sequencing, and DNAamplification. A DNA amplification method employing DNA polymerases thathas been particularly useful is the polymerase chain reaction (PCR)technique. The technique of PCR is described in numerous publications,including, PCR: A Practical Approach, M. J. McPherson, et al., IRL Press(1991), PCR Protocols: A Guide to Methods and Applications, by Innis, etal., Academic Press (1990), and PCR Technology: Principals andApplications for DNA Amplification, H. A. Erlich, Stockton Press (1989).PCR is also described in many U.S. Patents, including U.S. Pat. Nos.,4,683,195; 4,683,202; 4,800,159; 4,965,188; 4,889,818; 5,075,216;5,079,352; 5,104,792; 5,023,171; 5,091,310; and 5,066,584, which arehereby incorporated by reference; The PCR technique typically involvesthe step of denaturing a polynucleotide, followed by the step ofannealing at least a pair of primer oligonucleotides to the denaturedpolynucleotide, i.e., hybridizing the primer to the denaturedpolynucleotide template. After the annealing step, an enzyme withpolymerase activity catalyzes synthesis of a new polynucleotide strandthat incorporates the primer oligonucleotide and uses the originaldenatured polynucleotide as a synthesis template.

In many instances, a given DNA polymerase may fail to synthesize thedesired polynucleotide product. These failures may be attributable to anumber of reasons including such problems as template and primer basepair mismatches, lack of proofreading, insufficient rate of synthesis,high misincorporation rate, inability to transcribe GC or AT richregions, lack of sufficient processivity (processivity refers to thelength of synthesis product formed before the polymerase stopssynthesis), etc. It is therefore of interest to provide new methods andcompositions for improved polynucleotide synthesis over a wide varietyof experimental conditions.

SUMMARY OF THE INVENTION

The subject invention provides novel compositions containing a mixtureof (a) an enzyme that possesses substantial 3′-5′ exonuclease activityand (b) a DNA polymerase with less 3′-5′ exonuclease activity than theenzyme possessing substantial 3′-5′ exonuclease activity. Preferably,the enzyme with substantial 3′-5′ exonuclease activity is a DNApolymerase. Preferably, the DNA polymerase with less 3′-5′ exonucleaseactivity than the enzyme possessing substantial 3′-5′ exonucleaseactivity is a DNA polymerase substantially lacking 3′-5′ exonucleaseactivity. When a step in a technique of interest employingpolynucleotide synthesis involves the step of incubation at an elevatedtemperature, e.g., PCR, both the DNA polymerase and the enzyme withsubstantial 3′-5′ exonuclease activity are thermostable enzymes. Apreferred embodiment of the invention is a composition comprising theTaq DNA polymerase (from Thermus aquaticus) and the Pfu DNA polymerase(from Pyrococcus furiosus).

Another aspect of the invention is to provide methods for synthesizingpolynucleotides, typically DNA, using compositions comprising an enzymethat possesses substantial 3′-5′ exonuclease activity and DNA polymerasewith less 3′-5′ exonuclease activity than the enzyme with substantial3′-5′ exonuclease activity. Preferably, the DNA polymerase used in theprovided methods is a DNA polymerase that substantially lacks 3′-5′exonuclease activity. The methods of synthesizing DNA (or otherpolynucleotides) provided comprise the step of mixing a compositioncontaining (a) an enzyme possessing substantial 3′-5′ exonucleaseactivity and (b) a DNA polymerase with less 3′-5′ exonuclease activitythan the enzyme with substantial 3′-5′ exonuclease activity. Otherreagents required for polynucleotide synthesis include nucleotidetriphosphates (dNTPs), polynucleotide primers, a synthesis template, andthe like.

Another aspect of the invention is to use the subject method ofpolynucleotide synthesis to carry out the synthesis step in a polymerasechain reaction experiment.

Yet another aspect of the invention is to provide kits for the synthesisof polynucleotides, wherein the kits comprise an enzyme that possessessubstantial 3′-5′ exonuclease activity and a DNA polymerase with less3′-5′ exonuclease activity than the enzyme with substantial 3′-5′exonuclease activity, preferably a DNA polymerase substantially lacking3′-5′ exonuclease activity. Preferably, the enzyme with substantial3′-5′ exonuclease activity is a DNA polymerase. The kits may alsocontain polynucleotide precursors, synthesis primers, synthesistemplates, buffers, and the like.

DESCRIPTION OF SPECIFIC EMBODIMENTS

The subject invention provides novel composition for use in synthesizingpolynucleotides, particularly DNA. The subject compositions comprise anenzyme that possesses substantial 3′-5′ exonuclease activity and a DNApolymerase with less 3′-5′ exonuclease activity than the enzyme withsubstantial 3′-5′ exonuclease activity. In a preferred embodiment of theinvention, the DNA polymerase in the compositions is a DNA polymerasethat substantially lacks 3′-5′ exonuclease activity. The enzyme thatpossesses substantial 3′-5′ exonuclease activity is preferably a DNApolymerase. Prior to the inventors' work, DNA synthesis in vitro wasperformed with a single purified DNA polymerase. In a variety ofsynthesis procedures, the subject compositions provide superiorsynthesis results, as compared with the synthesis results obtained witha single DNA polymerase with less 3′-5′ exonuclease activity than theenzyme with 3′-5′ exonuclease activity alone (including synthesisresults obtained with DNA polymerases that substantially lack 3′-5′exonuclease activity).

Although compositions comprising a DNA polymerase with less 3′-5′exonuclease activity than the enzyme possessing substantial 3′-5′exonuclease activity may produce superior results in a variety ofsynthesis experiments, the composition is especially useful in DNAsynthesis when there exists one or more mismatched nucleotide(s),particularly mismatches at the 3′ end of one or more synthesisprimer(s). In such situations, the results achieved, i.e., the amount ofsynthesis product produced, are significantly greater than the amount ofsynthesis product obtained using either a DNA polymerase with less 3′-5′exonuclease activity than the enzyme possessing substantial 3′-5′exonuclease activity or with a DNA polymerase possessing substantial3′-5′ exonuclease activity alone. Other advantages of the subjectcompositions and methods include increased synthesis product yield,increased transcription product length, and the synthesis ofpolynucleotides that can not be synthesized by a given DNA polymerasealone.

The enzyme possessing substantial 3′-5′ exonuclease activity for use inthe subject compositions and methods may be any enzyme possessingsubstantial 3′-5′ single-stranded DNA exonuclease activity. Enzymespossessing substantial 3′-5′ exonuclease activity for use in the presentcompositions and methods may be isolated from natural sources orproduced through recombinant DNA techniques. Enzymes that possesssubstantial 3′-5′ exonuclease activity and their properties aredescribed in detail in, among other places, DNA Replication 2nd edition,Kornberg and Baker, supra and Enzymes, supra. Examples of enzymes thatpossess substantial 3′-5′ exonuclease activity include E. coliexonuclease I, E. coli exonuclease III, E. coli recBCD nuclease, mungbean nuclease, and the like. Preferred enzymes with substantial 3′-5′exonuclease activity for use in the subject compositions and methods areDNA polymerases that possess substantial 3′-5′ exonuclease activity.

DNA polymerases that possess substantial 3′-5′ exonuclease activityinclude the Pfu DNA polymerase, E. coli DNA polymerase I, Klenowfragment, T-4 polymerase, T-7 polymerase, E. coli DNA pol III, UltimaDNA Polymerase (Cetus), Vent DNA and Deep Vent DNA polymerases (NewEngland Biolabs). When using the subject compositions in reactionmixtures that are exposed to elevated temperatures, e.g., during the PCRtechnique, use of thermostable DNA polymerases is preferred. Examples ofthe thermostable DNA polymerases that possess substantial 3′-5′exonuclease activity include Vent DNA polymerase, Ultima DNA polymerase,Deep Vent DNA polymerase, and Pfu DNA polymerases. A particularlypreferred DNA polymerase possessing 3′-5′ exonuclease activity for usein subject composition is the Pfu DNA polymerase. The Pfu DNA polymeraseis commercially available from Stratagene (La Jolla, Calif.). A detaileddescription of the Pfu DNA polymerase can be found, among other placesin U.S. patent application Ser. No. 07/803,627 filed Dec. 2, 1991.

DNA polymerases and their properties are described in detail in, amongother places, DNA Replication 2nd edition, Kornberg and Baker, W.H.Freeman, New York, N.Y. (1991). DNA polymerases with less 3′-5′exonuclease activity for use in the subject compositions and methods maybe isolated from natural sources or produced through recombinant DNAtechniques. DNA polymerases with less 3′-5′ exonuclease activity thanthe 3′-5′ exonuclease activity of the enzyme with substantial 3′-5′exonuclease activity, i.e., 3′-5′ single-stranded exonuclease activity,include Taq DNA polymerases and Sequenase™ (modified bacteriophage T7DNA polymerase, available from U.S. Biochemical, Columbus, Ohio), andthe like. Additionally, the person of average skill in the art havingthe benefit of this disclosure will recognize that exonuclease deficientpolymerases such as Exo⁻ Pfu DNA polymerase, Vent® (exo⁻) DNApolymerase, Deep Vent® (exo-) DNA polymerase, and the like may besuitably used in the subject compositions. Taq DNA polymerase,Sequenase™, Exo⁻ Pfu DNA polymerase, Vent (exo⁻) DNA polymerase, andDeep Vent (exo⁻) DNA polymerase are all examples of DNA polymerases thatsubstantially lack 3′-5′ exonuclease activity.

When using the subject compositions in reaction mixtures that areexposed to elevated temperatures, e.g., during the PCR technique, use ofthermostable DNA polymerases is preferred. The subject composition mayalso be used with DNA polymerases that have not yet been isolated,provided that the DNA polymerases have less 3′-5′ single-stranded DNAexonuclease activity than the enzyme with substantial 3′-5′ exonucleaseactivity in the subject composition. Assays for both DNA polymeraseactivity and 3′-5′ exonuclease activity can be found in DNA Replication2nd Ed., Kornberg and Baker, supra, Enzymes, Dixon and Webb, AcademicPress, San Diego, Calif. (1979), as well as other publications availableto the person of ordinary skill in the art. A preferred DNA polymerasefor use in the subject compositions and methods of the invention is theTaq DNA polymerase.

The term “substantially lacking 3′-5′ exonuclease activity” when used inreference to a DNA polymerase, refers to those DNA polymerases that haveless 3′-5′ exonuclease activity than the enzyme included in the subjectcomposition that has substantial 3′-5′ exonuclease activity.

The term “thermostable” when used with respect to an enzyme, is readilyunderstood by a person of ordinary skill in the art. Typically, a“thermostable” enzyme retains at least 50 percent of its specificactivity after exposure to a temperature of 80° C. for a period of 20minutes.

The ratio of the DNA polymerase with less 3′-5′ exonuclease activitythan the enzyme possessing substantial 3′-5′ exonuclease activity to theenzyme possessing substantial 3′-5′ exonuclease activity in the subjectcomposition may be varied with respect to one another. The ratio of theDNA polymerase activity to 3′-5′ exonuclease activity present in thesubject composition employed in a given synthesis procedure may bereadily optimized by performing a series of simple experiments in whichthe ratio of the DNA polymerase with less 3′-5′ exonuclease activitythan the enzyme with substantial 3′-5′ exonuclease activity to theenzyme possessing substantial 3′-5′ exonuclease activity aresystematically varied with respect to one another and the synthesisresults compared.

The subject compositions may be used in various methods of synthesizingpolynucleotides in essentially the same manner as the DNA polymerasepresent in the subject composition. Typically, synthesis of apolynucleotide requires a synthesis primer, a synthesis template,polynucleotide precursors for incorporation into the newly synthesizedpolynucleotide, (e.g. dATP, dCTP, dGTP, dTTP), and the like. Detailedmethods for carrying out polynucleotide synthesis are well known to theperson of ordinary skill in the art and can be found, for example, inMolecular Cloning second edition, Sambrook et al., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1989). The process of PCRemploys a polynucleotide synthesis step in each cycle; thispolynucleotide synthesis step may be achieved using the subjectcompositions.

The invention herein also contemplates a kit format which comprises apackage unit having one or more containers of the subject compositionand in some embodiments including containers of various reagents usedfor polynucleotide synthesis, including synthesis in PCR. The kit mayalso contain one or more of the following items: polymerization enzymes,polynucleotide precursors, primers, buffers, instructions, and controls.Kits may include containers of reagents mixed together in suitableproportions for performing the methods in accordance with the invention.Reagent containers preferably contain reagents in unit quantities thatobviate measuring steps when performing the subject methods.

The following examples are offered for the purpose of illustrating, notlimiting, the subject invention.

Background of Examples

Characteristics of Taq and Pfu DNA Polymerases

Thermus aquaticus DNA Polymerase

Thermus aquaticus (Taq) DNA polymerase is a 94-kDa protein which doesnot have an inherent 3′ to 5′ exonuclease activity (Tindall, K. R., andT. A. Kunkel. 1988. Fidelity of DNA synthesis by the Thermus aquaticusDNA polymerase. Biochemistry 27:6008-6013). 3′ to 5′ exonucleaseactivity enables a polymerase to proofread and is therefore associatedwith fidelity of an enzyme. The estimated error rate of Taq varies from2×10′ mutations per nucleotide per cycle during PCR (Saiki, R. K., D. H.Gelfand, S. Stoffel, S. J. Scharif, R. Higuchi, G. T. Horn, K. B.Mullis, and H. A. Erlich. Primer-directed enzymatic amplification of DNAwith a thermostable DNA polymerase. 1988. Science 239:487491) to 2×10⁻⁵for nucleotide substitution errors in a single round of DNA synthesis ofthe lacZα gene (Eckert, K. A. and T. A. Kunkel. High fidelity DNAsynthesis by the Thermus aquaticus DNA polymerase. 1990. Nucleic AcidsRes. 18:3739-3744). The error rate of Taq DNA polymerase is important inpolymerization because it reflects the ability of the polymerase toextend from a mismatched primer:template. Taq DNA polymerase has beenshown to extend significantly less efficiently from a mismatched primer:template than from a correctly based paired primer:template (Innis, M.A., K. B. Myambo, D. H. Gelfand and M. A. D. Brow. DNA sequencing withThermus aquaticus DNA polymerase and direct sequencing of polymerasechain reaction-amplification of DNA. 1988. Proc. Natl. Acad. Sci. USA.85:9436-9440 and Kwok, S., D. E. Kellogg, D. Spasic, L. Goda, C.Levenson, and J. J. Sninsky. Effects of primer-template mismatches onthe polymerase chain reaction: Human immunodeficiency virus type I modelstudies. 1990. Nucleic Acids Res. 18:999-1005).

Taq DNA polymerase is highly processive at an extension rate of >60nucleotides per second at 70° C. on M13 phage DNA when using a GC-rich30 mer as a primer (Innis, et al. 1988). The Taq genome is 66.8% GC(Munster, M. J., A. P. Munster, J. R. Woodrow, and R. J. Sharp.Isolation and preliminary taxonomic studies of Thermus strains isolatedfrom Yellowstone National Park, USA. 1986. J of Gen. Microbiol.132:1677-1683).

Pyrococcus furiosus DNA Polymerase

Pyrococcus furiosus (Pfu) DNA polymerase is a 91-kDa protein which hasan inherent 3′ to 5′ exonuclease activity. This proofreading activityallows Pfu to extend from mismatched primer:templates by first removingthe mismatched base(s) followed by polymerization and results in anerror rate of 1.6×10⁻⁶ mutations per nucleotide per cycle in PCRreactions. The error rate of Pfu DNA polymerase is thus tenfold lowerthan that of Taq DNA polymerase and results in higher fidelity(Lundberg, K. S., D. D. Shoemaker, M. W. W. Adams, J. M. Short, J. A.Sorge, and E. J. Mathur. High-fidelity amplification using athermostable DNA polymerase isolated from Pyrococcus furiosus. 1991.Gene 108:1-6). The processivity of Pfu DNA polymerase is 10-15nucleotides per second and its genome is 38% GC.

Templates

cDNA Templates

cDNAs from 2 sources, hybridoma and PBLs (peripheral blood lymphocytes),were chosen as templates in these experiments. Hybridoma cDNA from humananti-tetanus toxoid 9F12 (ATCC, HM-8177) and mouse anti-humanfibronectin CG7C7 (ATCC, HB-126) express only one immunoglobulin heavyand light chain and therefore would contain a homogeneous population ofheavy and light chain cDNAs. The 9F12 cDNA had amplified efficiently inprevious experiments when using primers AB-61 or MK-205 with AB-76 (Fd)or MK-39 (VH), AB-25 and AB-94 (light chain[LC]), and MK-94 and AB-76(CH1). Based on nucleotide sequence, 9F12 is a human IgG1 from the VHIIIfamily with a kappa light chain. The SA-13 cDNA had amplifiedefficiently in previous experiments when using primers AB-19 with AB-41(Fd) and AB-25 and AB-26 (LC). PBL cDNA expresses immunoglobulin heavyand light chains from all of the human heavy and light chain families(Kabat, T. T. Wu, H. Bilofsky, M. Reid-Milner, and H. Perry, eds.Sequences of Proteins of Immunological Interest, 1987, U.S. PublicHealth Service, Washington, D.C.) and therefore would contain aheterogenous population of heavy and light chain cDNAs. This cDNA hadnot amplified efficiently with primer AB-61 or MK-205 with AB-76 (Fd) orMK-39 (VH) but had amplified efficiency with AB-25 and AB-94 (LC) andMK-94 and AB-76 (CH1) (Table 13).

DNA Templates

Nine different DNA templates were also used in these experiments. Thegenomic DNAs were isolated from human, Epstein Barr virus, Escherichiacoli, and transgenic and nontransgenic mouse. Plasmid DNAs werepBluescript II and pBluescript containing the light chain and Fd of ananti-tetanus toxoid immunoglobulin (Mullinax R. L., E. A. Gross, J. R.Amberg, B. N. Hay, H. H. Hogrefe, M. M. Kubitz, A. Greener, M.Alting-Mees, D. Ardourel, J. M. Short, J. A. Sorge, and B. Shopes. 1990.Identification of human antibody fragment clones specific for tetanustoxoid in a bacteriophage lambda immunoexpression library. Proc. Natl.Acad. Sci. USA 87:8095-8099).

Primer Design

The ability of an oligonucleotide to act as a primer in DNA synthesis isdependent on several factors: the kinetics of association anddissociation of the primer:template duplexes under the annealing andextension conditions, the effects of mismatched bases and their locationon duplex stability, and the efficiency with which the polymerase canrecognize and extend from a mismatched duplex. In general, single basepair mismatches at or near the terminal 3′ base of a primer are known toaffect the ability of the polymerase to bind and extend from theprimer:template and therefore should have a significant effect on theefficiency of the priming reaction.

In particular, Taq DNA polymerase requires that 3 to 5 bases at the 3′end of the primer base pair exactly in order for polymerization tooccur. The effect of other mismatches on the efficiency ofpolymerization is dependent on the number of mismatches and where theyoccur in the primer. This presents a problem when the exact templatesequence is not known such as when the nucleotide sequence of thetemplate is derived from amino acid sequence due to the redundancy ofthe amino acid code and when designing primers for templates of familiesof genes which are heterogeneous.

Four oligonucleotide primers designed to specifically prime the firstconstant region of human heavy chain immunoglobulin genes (VH) weredesigned based on the available nucleotide and amino acid sequences withthe problems above in mind (Mullinax, et al., 1990). Becauseexperimental results indicated poor priming and/or amplificationefficiency with PBL templates with Taq DNA polymerase, we wanted toinvestigate how this efficiency could be improved.

One of the human heavy chain first constant region primers, AB-61 (Table15) was chosen for examination. AB-61 has a dGTP as the 3′ base andwould require a dCTP in the corresponding position in the template inorder for efficient priming to occur when Taq DNA polymerase was usedfor primer extension due to its lack of 3′ to 5′ exonuclease activity(Kwok, et al. 1990, supra). However, Pfu DNA polymerase does have 3′ to5′ exonuclease activity and would remove any mismatched base(s) from the3′ end of the primer and would therefore be able to extend (Lundberg, etal. 1991, supra). Therefore it was of interest to investigate the effectof using Pfu DNA polymerase alone and in combination with Taq DNApolymerase in primer extension reactions using cDNA from hybridoma celllines (9F12 and CG7C7) and from human PBLs as the template under variousexperimental conditions.

Kwok, et al. (1990) demonstrated that primer extension efficiency whenusing Taq DNA polymerase is independent of the dNTP in the template whena dTTP is the 3′ base in the primer. Therefore the effect of theaddition of one or more dTTPs in various positions at the 3′ end of theprimer AB-61 (Table 13) was also investigated.

Buffer Comparisons

Buffer conditions have been shown to effect the processivity, activityand fidelity of polymerases. In particular, the processivity and/oractivity of Taq DNA polymerase are known to be affected by KCl, MgCl₂,(NH₄)₂SO₄, and NaCl concentrations. The fidelity of Taq DNA polymeraseis also affected by the concentration of MgCl₂ relative to the totalconcentration of dNTPs (Eckert, et al. 1990, supra) and dNTP and MnCl2concentrations (Leung, D. W., E. Chen, and D. V. Goeddel. 1989). Amethod for random mutagenesis of a defined DNA segment using a modifiedpolymerase chain reaction. Technique. 1:11-15).

Table 17 lists the buffer components and their concentrations for the10× Taq DNA polymerase and Pfu V25, #1, and #3 buffers used in theseexperiments.

Different Ratios of Taq and Pfu DNA Polymerases

Taq DNA polymerase is unable to correct nucleotide misincorporationsmade during polymerization due to its lack of 3′ to 5′ exonucleaseactivity. In general, this would result in the inability of Taq toextend from a newly polymerized strand annealed to a template when anincorrect nucleotide has been inserted. Pfu DNA polymerase has aninherent 3′ to 5′ exonuclease activity and would be able to remove theincorrectly inserted nucleotide and then extend from the correctly basepaired primer:template. The ratio of the two polymerases may be criticalfor optimal efficiency of this process. We therefore compared severalratios of Taq:Pfu DNA polymerases to determine the effect on DNAsynthesis from 3′ matched and mismatched primers.

In addition, Pfu DNA polymerase has been shown to degrade unannealedprimers by its 3′ to 5′ exonuclease activity. These degraded primerswould not be available in subsequent rounds of DNA amplification andwould therefore effect the efficiency of the PCR reaction. It maytherefore be desirable to have a low concentration of Pfu DNA polymeraserelative to Taq DNA polymerase to decrease this effect.

EXAMPLE 1

Primer Extension with Taq or Pfu DNA Polymerase In Separate Reactions

These experiments demonstrate the relative ability of Taq or Pfu DNApolymerase to PCR amplify hybridoma and PBL templates under variousconditions. Taq DNA polymerase resulted in either the presence of a PCRproduct or an increase in the amount of PCR product when compared to PfuDNA polymerase when amplifying hybridoma and PBL templates. In addition,the dNTP and not the MgCl₂ concentration affected the amount of LCproduct generated.

Taq and Pfu DNA Polymerases with CG7C7 Hybridoma Template

Taq and Pfu DNA polymerases were compared for their ability to amplifythe LC, CH1, and Fd regions of a mouse anti-human fibronectin antibody(CG7C7, ATCC HB-126). Total RNA was isolated from CG7C7 hybridoma cellsusing an RNA isolation kit (Stratagene). Five μg of total RNA wasconverted to cDNA in a first strand synthesis reaction using an oligo-dTprimer for the light chain and AB-41 for the heavy chain (Table 15).mRNA was annealed to the first strand primer at 65° C. for 5 minutesfollowed by cooling at room temperature for 30 minutes. First strandreactions were performed in 1× first strand buffer [1× first strandbuffer is 75 mM KCl; 50 mM tris-Cl, pH 8.3; 10 mM dithiothreitol; 3 mMMgCl₂; 1 Unit RNase Block II (Stratagene)], 375 μM each dNTP and 20Units Moloney-Murine Leukemia Virus Reverse Transcriptase (M-MLVRT)(Stratagene)] and incubated at 37° C. for 1 hour and then 42° C. for 30minutes.

PCR primers used to amplify the LC were AB-25 and AB-26, CH1 were MK-501and A-B-41, Fd were AB-41 and AB-19, and the polylinker region ofpBluescript were T3 and T7 (Table 14). PCR reactions with Taq DNApolymerase were at a primer concentration of 0.2 μM of each 5′ and 3′primer in 1× Taq buffer (Table 17) with 200 M each dNTP and 2.5 unitsTaq DNA polymerase (Stratagene; La Jolla, Calif.) using 1/10 of cDNAprepared in the first strand reaction as the template. Samples weredenatured at 99° C. for 5 minutes and annealed at 54° C. for 5 minutesfollowed by PCR amplification at 72° C. for 3 minutes, 93° C. for 1.5minutes and 54° C. for 2 minutes for 30 cycles.

PCR reactions with Pfu DNA polymerase were performed under the sameconditions but with 1× V25 buffer instead of Taq buffer.

Twenty μl of the 100 μl reaction was separated on an agarose gel byelectrophoresis and visualized by staining with ethidium bromide.Results are indicated by the relative amount of appropriately sized PCRproduct and all given in Table 1. TABLE 1 Taq and Pfu DNA polymeraseswith CG7C7 template V25 Taq buffer buffer Product Primers Taq Pfu FdAB-19/AB-41 2+ +/− CH1 MK-501/AB-41 2+ + LC AB-25/AB-26 + − polylinkerT3/T7 + −*The relative amounts of PCR product are indicated as a range of noproduct (−) to the most product (5+).

Results from this experiment indicate that only Taq DNA polymeraseproduced an appropriately sized PCR product with all of the primer pairsused. Pfu DNA polymerase produced either less or no product whencompared to Taq DNA polymerase with all of the primer pairs.

The CH1 primers were designed for amplification of constant regions ofthe antibody heavy chain and would be expected to base pair matchperfectly with their template. The T3 and T7 primers also base pairmatch perfectly with the pBluescript template.

Taq and Pfu DNA Polymerases with PBL Template

Taq DNA polymerase was used to amplify the LC (both kappa and lambda),CH1, CH2/CH3, and Fd regions of human PBL immunoglobulins. The MgCl₂ anddNTP concentrations were varied to try to increase the amount of PCRproduct generated. Total RNA was isolated from human PBLs using an RNAisolation kit (Stratagene). Five ug of total RNA was converted to cDNAin a first strand synthesis reaction using an oligo-dT primer for theLC, and MK-25 for the heavy chain. mRNA was annealed to the first strandprimer at 65° C. for 5 minutes followed by cooling at room temperaturefor 30 minutes. First strand reactions were performed in 1× first strandbuffer [1× first strand buffer is 75 mM KCl; 50 mM tris-Cl, pH 8.3; 10mM dithiothreitol; 3 mM MgCl₂; 1 Unit RNase Block II (Stratagene)], 375μM each dNTP and 20 Units Moloney-Murine Leukemia Virus ReverseTranscriptase (M-MLVRT) (Stratagene)] and incubated at 42° C. for 1hour.

PCR primers used to amplify the kappa LC were AB-25 and AB-26, lambda LCwere AB-92 and AB-28, CH2/CH3 were MK-25 and MK-26, Fd were AB-52 withAB-61, AB-62, AB-63, or AB-64 (Table 18). PCR reactions were at a primerconcentration of 0.2 μM of each 5′ and 3′ primer in 1× Taq buffer (Table17) with 2.5 units Taq DNA polymerase using 1/10 of cDNA prepared in thefirst strand reaction as the template. The kappa LC reaction was 2.0 mMMgCl₂ with 237.5 μM dNTPs, the lambda LC reaction was 1.8 mM MgCl₂ at137.5 μM or 237.5 μM dNTPs, the Fd reactions were 1.9 mM MgCl₂ with187.5 μM dNTPs, and the CH2/CH3 reactions were at 1.5 mM MgCl₂ with137.5 μM dNTPs. Samples were denatured at 94° C. for 5 minutes andannealed at 54° C. for 5 minutes followed by PCR amplification at 72° C.for 2.5 minutes, 93° C. for 1 minute and 54° C. for 1.5 minutes for 40cycles. Samples were analyzed as described above. Results are indicatedby the relative amount of appropriately sized PCR product and are givenin Table 2. TABLE 2 Taq and Pfu DNA polymerases with PBL template PBLtemplate 1.9 mM MgCl₂ 1.8 mM MgCl₂ 2.0 mM MgCl₂ 187.5 μM 137.5 μM 237.5μM 137.5 μM 237.5 μM primers product dNTP dNTP dNTP dNTP dNTPAB-61/AB-52 Fd − AB-62/AB-52 Fd − AB-63/AB-52 Fd − AB-64/AB-52 Fd −MK-25/MK-26 CH2/3 − − − − − AB-25/AB-26 kappa LC 4+ AB-92/AB-28 lambdaLC + 4+ + 4+

Only the kappa and lambda LC reactions produced a specific PCR product.The 1.8 and 2.0 mM MgCl₂ with 137.5 μM dNTP lambda LC reactions producedonly a very small amount of PCR product while the 1.8 and 2.0 mM MgCl₂with 237.5 μM dNTPs produced a large amount of PCR product. Thisindicates that the amount of PCR product in this experiment is relatedto the dNTP and not the MgCl₂ concentration. No PCR product wasgenerated with the Fd or CH2/CH3 primers under the conditions used.

EXAMPLE 2

Primer Extension Reactions with 3′ Mismatched Primers

These experiments investigated the ability of Taq and Pfu DNApolymerases both together and in separate reactions to extend fromprimers which contain one or two 3′ mismatches. The first experimentdemonstrates that Taq DNA polymerase can only extend from a primer whichmatches at the 3′ end under the conditions used (2.1 and 6.1 mM MgCl₂).The next experiment demonstrates that Taq and Pfu DNA polymerases usedin the same reaction will extend from all the primers with 3′ mismatchesthat were used from both hybridoma and PBL templates while neitherpolymerase alone was able to extend from all primers. The combination ofboth polymerases also resulted in more product in some of the samples.

This series of experiments suggest that Taq in Taq buffer will extendfrom a primer that is perfectly matched at the 3′ end, in V25 bufferwill extend from a primer that has one T which creates a mismatch at the3′ end of a primer, and in V25 buffer will not extend from a primer thathas two Ts which create two mismatches at the 3′ end of a primer. Taqand Pfu DNA polymerases in V25 buffer will extend from a primer that hastwo Ts which create a mismatch at the 3′ end of a primer.

It was also speculated that Taq and Pfu DNA polymerases may complementeach other in the reaction by polymerizing through A:T or G:C richregions of a template where one enzyme could not polymerize well throughboth types of regions. The Pfu genome is 38% GC while the Taq genome is66.8% GC.

Taq DNA Polymerase with 9F12 Template

The ability of Taq DNA polymerase to extend from primers with one ormore mismatches at the 3‘end’ was investigated. Nucleotide sequences ofthe 5′ primers based on the AB-61 primer and used to amplify 9F12 cDNAare given in Table 12. The 3′ primer in reactions which amplified the Fdportion of the human heavy chain was AB-76. The 3′ primer in reactionswhich amplified the VH portion of the human heavy chain was MK-39. Thelight chain 5′ VL primer was AB-25 and the 3′ CL primer was AB-94.

9F12 cDNA template was generated by isolating total RNA from thehybridoma cells using an RNA isolation kit (Stratagene). mRNA isconverted to cDNA in a first strand synthesis reaction using an oligo-dTprimer for the light chain and AB-76 for the heavy chain. The firststrand reactions was performed as described above except 200 units ofSuperscript (BRL; Gaithersburg, Md.)] was substituted for M-MLVRT andthe reactions were incubated at 42° C. for 1 hour.

PCR reactions were at a primer concentration of 0.2 μM of each 5′ and 3′primer in 1× Taq buffer (Table 17) with either 2.1 or 6.1 mM MgCl², 175μM each dNTP and 2.5 units Taq DNA polymerase using 1/10 of the cDNAprepared in the first strand reaction as the template. Samples weredenatured at 95° C. for 5 minutes and annealed at 54° C. for 5 minutesfollowed by PCR amplification at 72° C. for 3 minutes, 93° C. for 1.5minutes and 54° C. for 2.5 minutes for 40 cycles. Samples were analyzedas described above and the results are given in Table 3. TABLE 3 Taq DNApolymerase with 9F12 template Taq in Taq buffer primers product 2.1 mMMgCl₂ 6.1 mM MgCl₂ AB-61/AB-76 Fd 2+ − AB-714/AB-76 Fd − − AB-715/AB-76Fd − − AB-716/AB-76 Fd − − AB-717/AB-76 Fd − − AB-61/MK-39 VH 2+ +

PCR products of the appropriate size were generated only when AB-61 wasused as the 5′ primer. None of the 3′ mismatched primers generated a PCRproduct of the appropriate size although many unappropriately sizedproducts were made. Fd and VH products were generated in the reactioncontaining 2.1 mM MgCl₂ while only the VH was produced in the reactioncontaining 6.1 mM MgCl₂.

These results suggested that Taq DNA polymerase was not able to extendfrom 3′ mismatched primers under the conditions used and that increasingthe MgCl₂ concentration did not result in either an increase in PCRproduct, the ability to extend from 3′ mismatched primers, or generationof PCR products not made with 2.1 mM MgCl₂.

Taq and Pfu DNA Polymerases with 9F12 and PBL Templates

The next experiment investigated the effect of using Pfu and Taq DNApolymerases in the same PCR reaction to extend from primers with 3′matches and mismatches. The same primers were used (MK-205 which has thesame 21 bp on the 3′ end as AB-61 was substituted for AB-61) asdescribed above to amplify Fd, VH, CH1, and LC from PBL and 9F12 cDNAs.PCR reactions were performed in 1× V25 buffer (Table 17) with 200 μMeach dNTP and 2.5 units of both Taq and Pfu DNA polymerases or with PfuDNA polymerase alone using cDNA generated as described above from 9F12 &PBL RNA as the template. Samples were denatured at 94° C. for 5 minutesand annealed at 47° C. for 5 minutes followed by PCR amplification at71° C. for 3 minutes, 92° C. for 1 minute and 47° C. for 2.5 minutes for5 cycles and 71° C. for 3 minutes, 92° C. for 1 minute and 51° C. for2.5 minutes for 35 cycles. The lower annealing temperatures were used totry to improve primer:template annealing when mismatches occurred.Samples were analyzed as described above and the results are given inTables 4 and 5. TABLE 4 Taq and Pfu DNA polymerases with 9F12 and PBLtemplates V25 buffer 9F12 template PBL template Pfu/Taq Pfu primers FdVH Fd VH AB-61/AB-76 5+ 5+ + +/− AB-714/AB76 5+ 5+ 2+ +/− AB-715/AB76 2+5+ +/− +/− AB-716/AB76 5+ 5+ 2+ +/− AB-717/AB76 5+ 5+ + +/−

TABLE 5 9F12 PBL templates templates Pfu/Taq Pfu primers product Fd VHFd VH MK-94/AB-76 CH1 5+ +/− +/− AB-25/AB-94 LC +/− +/− +/−

An unexpected result in this experiment was that more amplificationproduct was generated when Taq and Pfu DNA polymerases were used in thesame PCR reaction in V25 buffer with both 9F12 and PBL cDNA as thetemplate. Numerous previous experiments using identical first strandsynthesis and PCR conditions with Taq DNA polymerase had resulted inonly a very small amount of Fd product generated from the same PBL mRNA.A very small amount of VH and CH1 products were generated using Pfu DNApolymerase alone in V25 buffer with PBL cDNA as a template.

Significant amounts of both Fd and VH PCR products were generated with9F12 cDNA as a template with all of the 5′ primers, including the 3′mismatched primers (AB-714 to AB-717), when both Taq and Pfu DNApolymerases were used. This contrasted with the previous experiment whenTaq DNA polymerase was not able to extend from the 3′ mismatched primers(AB-714 through AB-717) under the conditions used. These resultssuggested that Pfu DNA polymerase can remove 1-2 mismatched bases fromthe 3′ end of the primer. This would enable either Pfu or Taq DNApolymerase to extend from the perfectly base paired primer:template.

Taq and Pfu DNA Polymerases with 9F12 and PBL Templates

The above experiment was repeated to verify the results. The sameprimers were used to amplify Fd, CH1, and LC using PBL and 9F12 cDNAs astemplates. PCR reactions were performed in V25 buffer (Table 17) with200 μM each dNTP and 2.5 units of both Taq and Pfu DNA polymeraseseither together in the same reaction and or in separate reactions. PCRconditions were the same as described above and the results are given inTable 5. TABLE 6 Taq and Pfu DNA Polymerases with 9F12 and PBL TemplatesV25 buffer 9F12 template PBL template primers product Taq Pfu Pfu/TaqTaq Pfu Pfu/Taq AB-61/AB-76 Fd − − + − + − AB-714/AB-76 Fd 3+ − 4+ + −3+ AB-715/AB-76 Fd − − 2+ − − + AB-716/AB-76 Fd 4+ − 4+ 3+ + +AB-717/AB-76 Fd 2+ − 4+ + − 3+ MK94/AB-76 CH1 4+ 4+ 4+ 3+ − −AB-25/AB-94 LC 2+ − − + − −

PCR products generated with Pfu were Fd with MK-205 from PBL templateand CH1 from 9F12 template. PCR products generated with Taq were Fd withAB-714, AB-716, AB-717, CH1, and LC with PBL template and Fd withAB-714, AB-716, AB-717, CH1 and LC with 9F12 template. PCR productsgenerated with Pfu and Taq were Fd with MK-205, AB-714, AB-717 and avery small amount with AB-715 and AB-716 from PBL template. PCR productsgenerated with Pfu and Taq were Fd with AB-714, AB-715, AB-716, AB-717and CH1 from 9F12 template.

The amount of PCR product varied, however, in general more product wasgenerated with the 9F12 template than with the PBL template. This may bedue to the heterogeneity of the PBL template when compared to thehomogeneity of the 9F12 hybridoma template. When a homogeneous templateis amplified and the strand is not completed, it may anneal to itstemplate in a subsequent round of amplification and be extended to fulllength. When a heterogeneous template is amplified and the strand is notcomplete, the chances of it annealing to its original template in asubsequent round of amplification will be related to the heterogeneityof the templates present but will be less than that of a homogeneoustemplate. This may help explain why homogeneous templates produce morePCR product than heterogenous templates.

In this experiment Taq DNA polymerase was able to extend from the 3′mismatched primers which contain only a single mismatched base (AB-714,AB-716, and AB-717) but not one that has two mismatched bases (AB-715)with both the PBL and 9F12 cDNA templates. In a previous experiment, TaqDNA polymerase was not able to do this, however, these results areconsistent with the results of Kwok, et al. (1990, supra). Both AB-715and AB-717 contain 2 dTTPs at the 3′ end of the primer but in differentpositions. AB-715 replaces the last two dGTPs on the 3′ end and AB-717replaces the last dGTP and adds a dTTP to the 3′ end. Because thecorresponding base in the template is not known, the 3′ dTTP in AB-717may not create a mismatch with the template.

The V25 buffer used in this experiment had been made incorrectly and was5 mM KCl instead of 10 mM KCl. KCl concentration has been shown toeffect processivity and/or activity of Taq. This was corrected for allfuture experiments.

EXAMPLE 3

Effect of Different Ratios of Taq and Pfu DNA Polymerases on Extensionfrom 3′ Mismatched Primers

This experiment investigated different ratios of Taq and Pfu DNApolymerases and template concentrations when amplifying from perfectlymatched and 3′ mismatched primers. Plasmid DNA which encoded ananti-tetanus toxoid immunoglobulin fragment (kappa light chain and Fdportion of the heavy chain) was used as the template (Mullinax et al.1990, supra). Although optimal polymerase ratios and templateconcentrations were not identified in these experiments, additionalexperimentation would need to be done before concluding that they didnot have an effect.

Effect of Pfu DNA Polymerase Ratio on Extension from 3′ MismatchedPrimers

Five different ratios of Taq and Pfu DNA polymerases were used in PCRreactions with a combined total of 2.5 units per reaction. The ratioswere 9:1, 7:3, 5:5, 3:7, and 1:9 of Taq:Pfu. The Fd primers were AB-61,AB-715, and AB-717 in V25 buffer. Anti-tetanus toxoid plasmid DNAencoding a kappa LC and Fd was used as the template. Samples weredenatured at 95° C. for 7 minutes and annealed at 40° C. for 7-10minutes followed by PCR amplification at 72° C. for 2 minutes, 95° C.for 1 minute and 50° C. for 2 minutes for 30 cycles. Samples wereanalyzed as described above and results are given below. TABLE 7 EFFECTOF DIFFERENT RATIOS OF TAQ AND PFU DNA POLYMERASES ON EXTENSION FROM 3′MISMATCHED PRIMERS ratio of Taq:Pfu DNA polymerases primers product 10:09:1 7:3 5:5 3:7 1:9 0:10 AB-61/AB-76 Fd 4+ 5+ 5+ 5+ 5+ 4+ 4+AB-715/AB-76 Fd − 5+ 5+ 5+ 5+ 2+ 5+ AB-717/AB-76 Fd 2+ 5+ 5+ 5+ 5+ 5+ 5+

All PCR reactions generated a significant amount of PCR product withlittle variation except the reactions with AB-715 and AB-717 with TaqDNA polymerase alone and the reaction with Taq:Pfu at 1:9 with AB-715.All of the reactions which combine both Taq and Pfu DNA polymerases orcontain Pfu alone produced a significant amount of product. Taq DNApolymerase alone not would be expected to extend efficiently from the 3′mismatched primers.

Template concentration can affect the amplification efficiency and mayexplain there is little difference in the amount of PCR product in thedifferent samples when the ratio of DNA polymerases is varied. In thenext experiment, three different template concentrations were used totry to determine the effect of template concentration.

Effect of Template Concentration

Template concentrations were 100, 50, and 10 nanograms per reaction witheither 2.5 units of Taq or Pfu DNA polymerase in the reaction in V25buffer. The Fd primers were AB-61, AB-715, and AB-717 in V25 buffer.Samples were denatured at 95° C. for 7 minutes and annealed at 40° C.for 7-10 minutes followed by PCR amplification at 72° C. for 2 minutes,95° C. for 1 minute and 50° C. for 2 minutes for 30 cycles. Samples wereanalyzed as described above and results are given in Table 8. TABLE 8EFFECT OF TEMPLATE CONCENTRATION template concentration 100 ng 50 ng 10ng primers product Taq Pfu Taq Pfu Taq Pfu AB-61/AB-76 Fd 5+ 5+ 5+ 5+ 5+5+ AB-715/AB-76 Fd 5+ 5+ 5+ 5+ 5+ 5+ AB-717/AB-76 Fd 5+ 5+ 5+ 5+ 5+ 2+

Varying the template concentration did not seem to have an effect on theamount of PCR template generated except in the 10 ng template samplewith Pfu DNA polymerase alone with AB-717. The results seen previouslywith AB-715 where there was no amplification with Taq DNA polymerasealone was not reproduced and the experimenter indicated that an errorcould have been made. The experiment with AB-715 alone was repeated.

This experiment repeated the experiment described above using just theAB-715 primer under the same conditions. Samples were analyzed anddescribed above and results are given in Table 9. TABLE 9 EFFECT OFTEMPLATE CONCENTRATION template concentration 100 ng 50 ng 10 ng primerproduct Taq Pfu Taq Pfu Taq Pfu AB-715/AB-76 Fd 4+ 3+ 3+ 2+ 1+ 5+

The amount of PCR product generated correlated with templateconcentration in the reactions with Taq DNA polymerase alone and mayindicate that the template concentration affects amplificationefficiency from mismatched primers. No consistent effect could becorrelated with Pfu DNA polymerase.

EXAMPLE 4

Effect of Annealing Temperature on Extension from 3′ Mismatched Primers

The next experiment compared Taq and Taq with Pfu in Taq and V25 bufferswith mismatched primers at different annealing temperatures. Thisexperiment demonstrates that more PCR product is generated from aperfectly matched primer at a lower annealing temperature than at ahigher temperature. No product was produced with the primer with 2mismatches under any of the conditions used.

Effect of Annealing Temperatures of Extension from 3′ Matched andMismatched Primers

Taq and Taq with Pfu in Taq and V25 buffers with mismatched primers wereextended at different annealing temperatures. The Fd primers were AB-61and AB-715. cDNA templates were prepared from PBLs and 9F12. Sampleswere denatured at 95° C. for 5 minutes and annealed at either 48° C. or52° C. for 5 minutes followed by PCR amplification at 71° C. for 3minutes, 92° C. for 1 minute and 48° C. or 52° C. for 2.5 minutes for 5cycles and 71° C. for 3 minutes, 92° C. for 1 minute and 54° C. for 2.5minutes for 40 cycles. The lower annealing temperatures were useddetermine the effect the lower temperature had on primer:templateannealing when mismatches occurred. Samples were analyzed as previouslydescribed and results are given in Table 10. TABLE 10 Effect ofAnnealing Temperatures on Extension From 3′ Matched and MismatchedPrimers 9F12 template PBL template Taq buffer V25 buffer Taq buffer V25buffer primers product Taq Pfu/Taq Taq Pfu/Taq Taq Pfu/Taq Taq Pfu/Taqannealing at 48° C. (×5 cycles) and 52° C. (×35 cycles) AB-61/AB-76 Fd4+ 4+ 4+ 4+ +/− + − +/− AB-715/AB-76 Fd − − − − − − − − annealing at 54°C. (×40 cycles) AB-61/AB-76 Fd 4+ 4+ 2+ + − − − − AB-715/AB-76 Fd − − −− − − − −

PCR products generated with Pfu and Taq in Taq or V25 buffers were avery small amount of Fd using AB-61 with the PBL template at the lowerand not the higher annealing temperature. PCR products generated withTaq with and without Pfu in Taq or V25 buffer using AB-61 with the 9F12template resulted in more product at the lower rather than the higherannealing temperature. No PCR products were generated with the AB-715primer in any samples.

Results indicated that none of the polymerases or buffer combinationstested extended from the AB-715 primer. AB-61 and AB-715 differ by thedeletion of two dGTPs and the addition of two dTTPs at the 3′ end (Table13). The lower annealing temperatures did produce either the presence ofor an increase in the amount of PCR product generated.

EXAMPLE 5

PCR Reactions Using Primers Without 3′ Mismatches

The object of the experiments with the 3′ mismatched primers was todetermine PCR conditions would result in a sufficient amount of highfidelity PCR product to enable cloning of the encoded immunoglobulinfragments. Therefore, the original PCR primers designed to amplify allhuman heavy chain genes were now used in the PCR reactions with Taq andPfu DNA polymerases separately and in the same reaction. Resultsindicate that there was no significant difference in the amount of PCRproduct generated when either Taq or Taq and Pfu DNA polymerases wereused in these experiments.

Taq and Pfu DNA Polymerases with 9F12 and PBL Templates

The first strand synthesis and PCR reactions were performed as describedabove under PCR REACTIONS WITH 3′ MISMATCHED PRIMERS—Taq and Pfu DNApolymerases with 9F12 and PBL templates with the following change.AB-61, AB-62, AB-63, and AB-64 (Table 18) were used as the 5′ VHprimers. Samples were analyzed as described above and results are givenin Table 11. TABLE 11 Taq and Pfu DNA Polymerases With 9F12 and PBLTemplates V25 buffer 9F12 template PBL template primers product Taq PfuPfu/Taq Taq Pfu Pfu/Taq AB-61/AB-76 Fd 4+ − − 4+ +/− 4+ AB-62/AB-76 Fd4+ − 4+ 4+ +/− 4+ AB-63/AB-76 Fd 4+ + 4+ +/− − − AB-64/AB-76 Fd 4+ − 4+2+ − 2+ MK-94/AB-76 CH1 4+ 3+ 4+ 2+ − 3+ AB-25/AB-94 LC 2+ − 3+ − − +

PCR products generated with Pfu were a very small amount of Fd withAB-61 and AB-62 from PBL template and Fd with AB-63 and CH1 from 9F12template. PCR products generated with Taq were Fd with all 5′ primersand CH1 PBL and 9F12 templates and LC with 9F12 template. PCR productsgenerated with Pfu and Taq were Fd with AB-61, AB-62, AB-64, CH1, and LCfrom PBL template. PCR products generated with Pfu and Taq were Fd withAB-62, AB-63, AB-64, CH1, and LC from 9F12 template. In general, theresults with the PBL template had a lot of failure products and therewas significantly more product with the 9F12 template.

The inability of Pfu DNA polymerase to extend from any of the 5′ primersother than AB-63 may be due to internal mismatches with 9F12 as thetemplate and not be due to the 3′ primer:template mismatches.

EXAMPLE 6

The effect of a combination of four different polymerases in sevendifferent buffers was tested on three different templates. The desiredeffects were an increase in the amount of PCR product generated and/oran increased specificity of amplification. No effect was observedbetween using a combination of four polymerases and Taq DNA polymerasein the buffers tested.

Seven different templates with eight different primer sets were used inthis experiment. The genomic DNAs were isolated from human, Epstein Barrvirus, Escherichia coli, and transgenic and normal mouse. Plasmid DNAswere pBluescript II and pBluescript containing the light chain and Fd ofan anti-tetanus toxoid immunoglobulin (Mullinax et al., 1990, supra).Primer sequences and their respective DNA templates are given in Table16. The thermostable polymerases used in this experiment were Taq, Exo⁺and Exo⁻ Pfu, and ES-4 DNA polymerases (Stratagene; La Jolla, Calif.) atfinal concentrations of 2.5, 1.25, 1.25, and 0.125 units per reaction,respectively. PCR reactions were at a primer concentration of 0.2 μM ofeach 5′ and 3′ primer in 1× Taq buffer, 1× Pfu #1, or 1× Pfu #3 (Table17) with 200 μM each dNTP. An additional reaction with Taq DNApolymerase in 1× Taq buffer was also performed. Samples were denaturedat 95° C. for 5 minutes and annealed at 40° C. for 5 minutes followed byPCR amplification at 95° C. for 0.5 minutes, 40° C. for 1.5 minutes and68° C. for 3 minutes for 25 cycles. Samples were analyzed as previouslydescribed and results are not given.

Results indicated that no significant increase in the amount of PCRproduct generated or an increase in specificity was observed whencomparing Taq DNA polymerase in Taq buffer and a combination ofpolymerases in the three different buffers tested. Results seemed tocorrelate with the buffer used and not the polymerase.

EXAMPLE 7

Taq and Pfu DNA Polymerases In Splice Overlap Extension Reactions toGenerate Cloning Vectors

A series of lambda-based vectors were constructed to expressimmunoglobulin fragments on the surface of M13 phage. The exampledescribed below describes the construction of one of these vectors. Pfuand Taq DNA polymerases in combination were used to construct thisvector because of the high processivity of Taq DNA polymerase and thehigh fidelity of Pfu DNA polymerase. The nucleotide sequence of thecpVIII expression vector matched the expected nucleotide sequence.

cpVIII expression vector construction

Oligonucleotide primers used to construct the IZ H-8 (−1 to 50) vectorwith the cpVIII protein domain were designed to encode the following: anXho I restriction site, stop codons, nucleotide spacer sequences, an XbaI site that generates an amber codon, amino acids −1 to 50 of cpVIII,stop codons, and a Spe I restriction site.

Nucleotide sequences of the primers used to amplify cpVIII from M13Phagescript DNA (Stratagene; La Jolla, Calif.) using the 5′ and 3′cpVIII primers are given in Table 19. All PCR reactions were at a primerconcentration of 0.2 μM of each 5′ and 3′ primer in 1× V25 buffer with200 μM each dNTP and 2.5 units each Taq and Pfu DNA polymerases. Sampleswere denatured at 95° C. for 5 minutes and annealed at 54° C. for 5minutes followed by PCR amplification at 74° C. for 3 minutes, 93° C.for 1.5 minutes and 54° C. for 2.5 minutes for 30 cycles.

The cpVIII encoding PCR product was restriction digested with Xho I andSpe I and ligated into the IZ H vector (Stratacyte; La Jolla, Calif.;Huse, W. D., L. Sastry, S. A. Iverson, A. S. Kang, M. Alting-Mees, D. R.Burton, S. J. Benkovic, and R. A. Lerner. Generation of a largecombinatorial library of the immunoglobulin repertoire in phage lambda.1989. Science. 246:1275-1281) which had previously been restrictiondigested with Xho I and Spe I. The ligation products were packaged withGigapack II® Gold (Stratagene; La Jolla, Calif.) and plated withXL1-Blue host cells. The desired construct was identified by PCRamplification of isolated phage cores with the 5′ and 3′ cpVIII cloningprimers, converted to the plasmid format by in vivo excision with VCSM13 helper phage (Short, J., J. M Fernandez, J. A. Sorge, and W. D.Huse, Lambda ZAP: a bacteriophage lambda vector with in vitro excisionproprites, 1988, Nucleic Acids Res. 16:7583-7600) and the nucleotidesequence was determined by the dideoxy method. The nucleotides wassequence as expected. TABLE 12 HUMAN HEAVY CHAIN PCR PRIMERS WITHMATCHED AND 3′ MISMATCHES VH PRIMERS primer description nucleotidesequence (5′ to 3′) AB-205 5′ VH GTCCTGTCCGAGGTGCAGCTGCTCGAGTCTGG (SEQID NO: 1) AB-61 5′ VH AGGTGCAGCTGCTCGAGTCTGG (SEQ ID NO: 2) AB-714 5′ VHAGGTGCAGCTGCTCGAGTCTGT (SEQ ID NO: 3) AB-715 5′ VHAGGTGCAGCTGCTCGAGTCTTT (SEQ ID NO: 4) AB-716 5′ VHAGGTGCAGCTGCTCGAGTCTGGT (SEQ ID NO: 5) AB-717 5′ VHAGGTGCAGCTGCTCGAGTCTGTT (SEQ ID NO: 6) AB-76 3′ CH1AGCATCACTAGTACAAGATTTGGGCTC (SEQ ID NO: 7) AB-52 3′ CH1CGGGAGATCATGAGGGTGTCCTT (SEQ ID NO: 8) MK-39 3′ VHATATACTAGTGAGACAGTGACCAGGGTTCC (SEQ ID NO: 9) TTGGCCCCA

TABLE 13 HUMAN HEAVY AND LIGHT CHAIN PCR PRIMERS primer descriptionnucleotide sequence (5′ to 3′) AB-205 5′ VHGTCCTGTCCGAGGTGCAGCTGCTCGAGTCTG (SEQ ID NO: 1) G AB-61 5′ VHAGGTGCAGCTGCTCGAGTCTGG (SEQ ID NO: 2) AB-714 5′ VHAGGTGCAGCTGCTCGAGTCTGT (SEQ ID NO: 3) AB-715 5′ VHAGGTGCAGCTGCTCGAGTCTTT (SEQ ID NO: 4) AB-716 5′ VHAGGTGCAGCTGCTCGAGTCTGGT (SEQ ID NO: 5) AB-717 5′ VHAGGTGCAGCTGCTCGAGTCTGTT (SEQ ID NO: 6) AB-76 3′ CH1AGCATCACTAGTACAAGATTTGGGCTC (SEQ ID NO: 7) AB-52 3′ CH1CGGGAGATCATGAGGGTGTCCTT (SEQ ID NO: 8) MK-39 3′ VHATATACTAGTGAGACAGTGACCAGGGTTCC (SEQ ID NO: 9) TTGGCCCCA AB-25 5′ VLGTGCCAGATGTGAGCTCGTGATGACCCAGT (SEQ ID NO: 10) CTCCA AB-94 3′ CLTCCTTCTAGATTACTAACACTCTCCCCTGTT (SEQ ID NO: 11)GAAGCTCTTTGTGACGGGCGAACTC MK-94 5′ CH1 GTCTCACTAGTCTCCACCAAGGGCCCATCGG(SEQ ID NO: 12) TC AB-58 3′ CH2 CGGGAGATCATGAGGGTGTCCTT (SEQ ID NO: 13)MK-25 5′ CH2 CTCAGTATGGTGGTTGTGC (SEQ ID NO: 14) MK-26 3′ CH3CCGGAATTCTTATCATTTACCCGGAGA (SEQ ID NO: 15)* nucleotides in bold indicate where dTTP was introduced into the AB-61primer

TABLE 14 pBluescript PCR primers description nucleotide sequence (5′ to3′) T3 ATTAACCCTCACTAAAG (SEQ ID NO: 16) T7 AATACGACTCACTATAG (SEQ IDNO: 17)

TABLE 15 MOUSE HEAVY AND LIGHT CHAIN PCR PRIMERS primer descriptionnucleotide sequence (5′ to 3′) AB-25 5′ VL kappaGTGCCAGATGTGAGCTCGTGATGACCC (SEQ ID NO: 10) AGTCTCCA AB-26 3′ CL kappaTCCTTCTAGATTACTAACACTCTCCCCT (SEQ ID NO: 18) GTTGAA AB-28 5′ VL lambdaCTGCACAGGGTCCTGGGCCGAGCTCGT (SEQ ID NO: 19) GGTGACTCAG AB-92 3′ VLlambda GCATTCTAGACTATTAACATTCTGTAGG (SEQ ID NO: 20) GGC AB-19 5′ VHAGGTCCAGCTGCTCGAGTCTGG (SEQ ID NO: 21) AB-41 3′ CH1AGGCTTACTAGTACAATCCCTGGGCAC (SEQ ID NO: 22) AAT MK-501 3′ VHCCGTTACTAGTAGCCAAAACGACACCC (SEQ ID NO: 23) CCATCTGTC

TABLE 16 DNA TEMPLATES AND PCR PRIMER SEQUENCES primer nucleotidesequence template description description (5′ to 3′) human 5′ Gaudier'sCCTGAGGGCTCCCAGAGAGT (SEQ ID NO: 24) disease GG human 3′ Gaucher'sdisease GGTTTAGCACGACCACAACA (SEQ ID NO: 25) GC pBluescript KS+ 5′multiple cloning ATTAACCCTCACTAAA (SEQ ID NO: 26) site pBluescript KS+3′ multiple cloning AATACGACTCACTATAG (SEQ ID NO: 27) site Epstein Barrvirus 5′ nuc antigen gene GGCTGGTGTCACCTGTGTTA (SEQ ID NO: 28) EpsteinBarr virus 3′ nuc antigen gene CCTTAGGAGGAACAAGTCCC (SEQ ID NO: 29) E.coli 5′ RNase H gene CTTGAAGATCTATGCTTAAA (SEQ ID NO: 30) CAGGTAG E.coli 3′ RNase H gene CATGTGAATTCTTAAACTTC (SEQ ID NO: 31) AACTTGGtransgenic mouse 5′ lambda lacZ insert GGTGGCGACGACTCCTGGAG (SEQ ID NO:32) CCC transgenic mouse 3′ lambda lacZ insert GACAGTCACTCCGGCCCGTG (SEQID NO: 33) CGG human 5′ fucosidase gene AAGCTTCAGGAAAACAGTG (SEQ ID NO:34) AGCAGCGCCTC human 3′ fucosidase gene AGTCAGGTATCTTTGACAGT (SEQ IDNO: 35) nontransgenic 5′ B-adrenergic GGAATTCGTAACAGGACTTA (SEQ ID NO:36) mouse receptor CGGTAGC nontransgenic 3′ B-adrenergicAGCACTCATAAGTGACACCC (SEQ ID NO: 37) mouse receptor transgenic mouse 5′lambda lacI insert CATAGCGAATTCGCAAAACC (SEQ ID NO: 38) TTTCGCGGTATGGtransgenic mouse 3′ lambda lacI insert ACTACGGAATTCCACGGAAA (SEQ ID NO:39) ATGCCGCTCATCC

TABLE 17 10x PCR BUFFER COMPONENTS component Taq V25 Pfu #1 Pfu #3 KCl500 mM 100 mM 100 mM 100 mM (NH₄)₂SO₄ 60 mM 60 mM 100 mM tris-Cl, 100 mMpH 8.8 tris-Cl, 200 mM 200 mM pH 8.2 tris-Cl, 200 mM pH 8.5 MgCl2 15 mM15 mM 20 mM 15 mM MgSO4 20 mM Triton X-100 1% (v/v) 1% (v/v) 1% (v/v)bovine serum 100 μg/ml 100 μg/ml 1 mg/ml albumin gelatin 0.01% (w/v)

TABLE 18 HUMAN VH PCR PRIMERS primer description nucleotide sequence (5′to 3′) AB-61 5′ VH AGGTGCAGCTGCTCGAGTCTGG  (SEQ ID NO: 2) AB-62 5′ VHAGGTGCAGCTGCTCGAGTCGGG (SEQ ID NO: 40) AB-63 5′ VHAGGTGCAACTGCTCGAGTCTGG (SEQ ID NO: 41) AB-64 5′ VHAGGTGCAACTGCTCGAGTCGGG (SEQ ID NO: 42)

TABLE 19 OLIGONUCLEOTIDE PRIMERS USED TO CONSTRUCT THE IZ H-8 (−1 to 50)VECTOR 5′ cpVIII TTGACTCGAGTAATCTGAGCTAAA (SEQ ID NO: 43)GTCTAGAGCGCTGAGGGTGACGATCC CC 3′ cpVIII ATGGCAACTAGTTATCAGCTTGCT (SEQ IDNO: 44) TTCGAGG

EOUIVALENTS

All publications and patent applications mentioned in this specificationare indicative of the level of skill of those skilled in the art towhich this invention pertains. All publications and patent applicationsare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

The foregoing written specification is considered to be sufficient toenable one skilled in the art to practice the invention. Indeed, variousmodifications of the above-described modes for carrying out theinvention which are obvious to those skilled in the field of molecularbiology or related fields are intended to be within the scope of thefollowing claims.

1-32. (canceled)
 33. A composition comprising a mixture comprising: (a)an enzyme possessing 3′ to 5′ exonuclease activity, and (b) a DNApolymerase which has reverse transcriptase activity, wherein thepolymerase has less 3′ to 5′ exonuclease activity than the enzyme.
 34. Acomposition according to claim 33, wherein the enzyme possessing 3′ to5′ exonuclease activity is a DNA polymerase.
 35. A composition accordingto claim 33, wherein the enzyme possessing 3′ to 5′ exonuclease activityis a fragment of a DNA polymerase.
 36. A composition according to claim33, wherein both the enzyme possessing 3′ to 5′ exonuclease activity andthe DNA polymerase are thermostable.
 37. A composition comprising amixture comprising: (a) an enzyme possessing 3′ to 5′ exonucleaseactivity, and (b) a DNA polymerase which is a reverse transcriptase,wherein the polymerase has less 3′ to 5′ exonuclease activity than theenzyme.
 38. A composition according to claim 37, wherein the enzymepossessing 3′ to 5′ exonuclease activity is a DNA polymerase.
 39. Acomposition according to claim 37, wherein the enzyme possessing 3′ to5′ exonuclease activity is a fragment of a DNA polymerase.
 40. Acomposition according to claim 37, wherein both the enzyme possessing 3′to 5′ exonuclease activity and the DNA polymerase are thermostable.